Yuhang Guo

[feature request] Genotyping more than 500 samples

3

I need to make a genotyping more than 500 samples, I hope the software can add this feature

[ISSUE] KMC stopped at stage1

10

1. Issue: when I run kmc ,it increase to 100%,and then stopped 2. command line is kmc -k55 -ci1 -m1000 -t120 -sr120 -fbam /data/map_res/trimmed-SK/P2.sorted.bam ./00-kmc-res/P2.sorted.bam ./kmc-tmp/ I have set such...

How to specify the version for Plants.ensemble ?

1

I need to annote DEGs for Zea Maize of version 38, however the latest version is 52. My code is: `plants R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under:...

## Bug Report ### Affected tool(s) or class(es) gatk HaplotypeCaller _--do-not-run-physical-phasing false_ ### Affected version(s) gatk-4.4.0.0 ### Description I used **gatk HaplotypeCaller** with parameter _--do-not-run-physical-phasing false_, some missing genotypes were...

I converted vcf file to fasta file, then I used **_Treebest_** to build NJ tree with command " treebest nj -W -t ntmm -b 1000 fastfile > result", Error occurred:...

``` library(ChIPseeker) require(GenomicFeatures) GFF_PATH = 'f:/07-CAUS/01-Linux-service/Maize_reference/B73-Ensembl-V4-48/Zea_mays.B73_RefGen_v4.48.gff3.gz' maizev4.db

Delly Results Can't Annotation and Visualization completely

1

Delly have updated to version 0.8.7. I used delly-0.8.7 to call SV, but some SVs were not included in "readDelly", maybe there are some bugs with version compatibility. Attached is...

how to install hdf 1.8.0 or above?

1

I tried many times to install hdf 1.8.0 but i still can't build blasr. many error may occured by gcc version ,I want to know which version are you used...